The complexity of the network, with crews and aircraft right across the UK doesn’t help a small operation. Flybe has 8 aircraft over two hubs with multiple one stops to offline locations and night stops. Overnighting at an airport not connected to a home base is a brave thing as schedule recovery is doubly complex. 75% of Heathrow destinations not connecting hubs is also foolish.
emerald has 14 aircraft over two hubs. All aircraft are home every evening and no one stop services.
If things go wrong, and they do, Flybe has less capability to recover as quickly.